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Topic: Manmade Software is Clumsy Compared to Godmade Software (Read 982 times) previous topic - next topic

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  • JonF
Re: Manmade Software is Clumsy Compared to Godmade Software
Reply #25

Quote
World J Biol Chem. 2014 Aug 26; 5(3): 275-278.
Published online 2014 Aug 26. doi:  10.4331/wjbc.v5.i3.275
PMCID: PMC4160521
Life is more than a computer running DNA software
František Baluška and Guenther Witzany

Are cellular organisms only robot-like computing machines that function strictly according to their algorithm-based programming? Or, rather, are they coordinated complex entities that share bio-communication properties that may vary according to different context-specific needs? Is DNA the unequivocal syntax for sequences out of which one can construct living cells, viruses and phages for a household appliance? Or is the superficial molecular syntax of DNA solely the result of evolution's long inserts and deletions of an abundance of various genetic parasites that shape host genomes? The most crucial questions are: do DNA sequences contain a hidden deep grammar structure that varies according to the meaning and context of environmental insults; do DNA sequences match with high fidelity environmental circumstances that led to epigenetic markings and memory? If yes, this would then mean that the identical DNA sequence may have various-even contradictory-meanings. In fact, this scenario is emerging as true[4-8].

EPIGENETICS: HIDDEN DEEP GRAMMAR
Interestingly, in complex genomes like humans, the coding genes are about 1.5% of the total genome whereas the abundance of non-coding RNAs are about 98.5%. This means Craig Venter's household appliance box could focus only on the 1.5% coding sequences. The DNA sequences of genomes do not represent 1:1 depictions of unequivocal coding structures such as genes, but in light of the variety of epigenetic markings-with its executives RNA editing and alternative splicing-can store a multitude of further meanings[4-8].

This means epigenetic marking saves energy costs like in human language. A limited repertoire of signs, and a limited number of rules to combine these signs correctly, enables signs using agents to generate an unlimited number of sentences with a superficial grammar in the visible text and an abundance of connotations by marking through gestures and other conscious and unconscious bodily expressions such as the movements of three hundred different eye muscles[9].

...

Therefore, DNA organized in chromatin is far more complex than the human-made "software system", except that we are confusing the algorithm-based simulation of real-life storage with the real life, the computer machines with the living cells and organisms, and the self-reproducing automatons with the real-life organisms that can replicate since the origins of life[5,9,14].

...

The genome itself, via natural genome editing[19], generates large amounts of coherent new sequences and inserts these into DNA genomes without damaging essential protein-coding regions. This is not possible for any human-made software.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4160521/
The best designs are simple.
Complexity is a sign of bad design.
Simplicity is hard. Complexity is something that happens if you don't prevent it.

Also, this
Quote
The genome itself, via natural genome editing[19], generates large amounts of coherent new sequences and inserts these into DNA genomes without damaging essential protein-coding regions. This is not possible for any human-made software.
is nonsense. Software used to work like that, it turned out be be a spectacularly bad idea. We stopped doing it that way.
Hahahahahaha

Yeah ... organisms don't operate very well ... if God would just update the software ...

Lolololol
That's all you got out of that?

Moran.
"I would never consider my evaluation of his work to be fair minded unless I had actually read his own words." - Dave Hawkins

Re: Manmade Software is Clumsy Compared to Godmade Software
Reply #26
Here is a quick and dirty version, Dave:

First a short preamble:

Biological organisms reproduce themselves, with variance, i.e. offspring are close enough to their parents that we can call it "reproduction" but there are always small differences.  These small variations have lots of different causes, but quite a lot of them are due to the offspring having slightly different DNA sequences to the parent.

Let's for now talk about sexually reproducing organisms to keep things simple-ish.  Sexually reproducing organism produce offspring that have some features of one parent and some features from another.  The combination itself makes them unique. But the combination at genetic level means that sometimes brand-new genetic sequences are generated.  Other mechanisms can also result in novel sequences.

Now for the main point:

As with Joe Hopping's sheep, sometimes a variant will appear with no obvious reproductive advantage or disadvantage to the organism.  Dark, slow-growing hooves for instance, instead of lighter, faster growing hooves.  Because there's no clear advantage or disadvantage, populations of these sheep will have some dark-hooved individuals and some light-hooved ones.  Then a specific population finds itself owned by Joe Hopping.  Now light hooves are seriously disadvantageous, because Hopping doesn't let them breed.  He only breeds from the dark-hooved ones.

But you know this.  You also know that this happens NATURALLY - instead of being owned by Joe Hopping, the sheep may find themselves in a very boggy environment, where their hooves don't wear down easily, and they also trap what my grandmother called gubbins.  So they tend to get infected feet.  So the dark-hooved onces have a reproductive advantage.

In other words, the population genome becomes OPTIMISED for boggy ground by dint of that population mostly bearing the dark-hooved sequence.  Rinse and repeat, over and over, and you end up with shorter/longer horns, thicker/thinner wool etc.

Great system for optimisation.  In the process lots of other not very useful variants appear.  They get weeded out if they are actually harmful, but not if they don't.  They just sit there in the population doing nothing, until the environment changes in a way that they are either useful, in which case they will become more prevalent, or disadvantageous, in which case they will become less so.  Or they may just hang around to delight us with variety.

That method of optimising a genome is not the way a human designer would do it.  There are loads of disadvantages.  You get lots of redundant code.  And you can't transfer good bits of code into other bits of code very easily to get the best of both worlds (sexual reproduction isn't a very efficient means of horizontal transfer).  And you waste a lot of sheep and time.

But it doesn't matter because you have plenty of sheep and time.

A human designer doesn't.  So a human designer has to figure out what is needed, as efficiently as possible.  She has to decide on a single solution quite quickly - she can't afford to experiment with weird and unlikely solutions of no obvious immediate benefit.  She doesn't want to write a whole bunch of redundant code. 

However, what she can do, is easily splice bits of code in from some other programme.  She can make the code quite modular in fact, and call on lots of existing functions, many developed by different teams for different purposes.  And she expects them to be easily understood and readable, and not be full of irrelevant extra stuff.

So to her, a sheep genome, even of one of Hopping's sheep, would look like "bad code".  Lots of useless stuff, some of it potentially useful for some non-obvious purpose, lots of it simple leftover junk.  And she'd find it was virtually impossible to transfer any of it to anything other than a subsequent version of the code.  No swapping anything other than tiny bits over into somebody else's code.

In other words: human software looks like it's been designed by and for human designers.  Biological genomes look like they evolved.

The first shows evidence of the limitations and non-limitations of human designers.  the second shows evidence of the limitations and non-limitations of evolution.

Which is why most people find the ID argument pretty flawed.  The very things that DON'T look like the way humans design things are the very things that are TYPICAL of things that have been optimised by evolution.  Which is a pretty good system.
Some of what you say here is true.  One thing you seem to miss is - as Ayala observed in that quote that I wheel out every so often - most of the variation we see in organisms already exists within the respective genomes.  What does NOT exist previously within genomes is random stuff - mistakes - which the cell is designed to rigorously try to prevent.  And it does a damn good job, but not perfect as we have often discussed.  So mistakes happen and so we do get new variants.  And there are almost zero examples out of trillions of any of these random variants that can be in any way spun as being "beneficial" to the organism or the population.  The number may actually be zero now as we have learned more (for example, antibiotic resistance in bacteria used to be the "textbook example" of random mutations being beneficial but that crashed and burned). 

The more we learn about genomes, the more we realize that this amazing adaptive system that your describe HAS ALWAYS BEEN THERE.  IOW, we don't have any evidence of it having NOT been there ... EVER.  Any speculation that it wasn't at some point in the past is just that ... speculation ... and pretty stupid speculation at that.  That idea flies in the face of all reason and logic and experience.

  • RAFH
  • Have a life, already.
Re: Manmade Software is Clumsy Compared to Godmade Software
Reply #27
Here is a quick and dirty version, Dave:

First a short preamble:

Biological organisms reproduce themselves, with variance, i.e. offspring are close enough to their parents that we can call it "reproduction" but there are always small differences.  These small variations have lots of different causes, but quite a lot of them are due to the offspring having slightly different DNA sequences to the parent.

Let's for now talk about sexually reproducing organisms to keep things simple-ish.  Sexually reproducing organism produce offspring that have some features of one parent and some features from another.  The combination itself makes them unique. But the combination at genetic level means that sometimes brand-new genetic sequences are generated.  Other mechanisms can also result in novel sequences.

Now for the main point:

As with Joe Hopping's sheep, sometimes a variant will appear with no obvious reproductive advantage or disadvantage to the organism.  Dark, slow-growing hooves for instance, instead of lighter, faster growing hooves.  Because there's no clear advantage or disadvantage, populations of these sheep will have some dark-hooved individuals and some light-hooved ones.  Then a specific population finds itself owned by Joe Hopping.  Now light hooves are seriously disadvantageous, because Hopping doesn't let them breed.  He only breeds from the dark-hooved ones.

But you know this.  You also know that this happens NATURALLY - instead of being owned by Joe Hopping, the sheep may find themselves in a very boggy environment, where their hooves don't wear down easily, and they also trap what my grandmother called gubbins.  So they tend to get infected feet.  So the dark-hooved onces have a reproductive advantage.

In other words, the population genome becomes OPTIMISED for boggy ground by dint of that population mostly bearing the dark-hooved sequence.  Rinse and repeat, over and over, and you end up with shorter/longer horns, thicker/thinner wool etc.

Great system for optimisation.  In the process lots of other not very useful variants appear.  They get weeded out if they are actually harmful, but not if they don't.  They just sit there in the population doing nothing, until the environment changes in a way that they are either useful, in which case they will become more prevalent, or disadvantageous, in which case they will become less so.  Or they may just hang around to delight us with variety.

That method of optimising a genome is not the way a human designer would do it.  There are loads of disadvantages.  You get lots of redundant code.  And you can't transfer good bits of code into other bits of code very easily to get the best of both worlds (sexual reproduction isn't a very efficient means of horizontal transfer).  And you waste a lot of sheep and time.

But it doesn't matter because you have plenty of sheep and time.

A human designer doesn't.  So a human designer has to figure out what is needed, as efficiently as possible.  She has to decide on a single solution quite quickly - she can't afford to experiment with weird and unlikely solutions of no obvious immediate benefit.  She doesn't want to write a whole bunch of redundant code. 

However, what she can do, is easily splice bits of code in from some other programme.  She can make the code quite modular in fact, and call on lots of existing functions, many developed by different teams for different purposes.  And she expects them to be easily understood and readable, and not be full of irrelevant extra stuff.

So to her, a sheep genome, even of one of Hopping's sheep, would look like "bad code".  Lots of useless stuff, some of it potentially useful for some non-obvious purpose, lots of it simple leftover junk.  And she'd find it was virtually impossible to transfer any of it to anything other than a subsequent version of the code.  No swapping anything other than tiny bits over into somebody else's code.

In other words: human software looks like it's been designed by and for human designers.  Biological genomes look like they evolved.

The first shows evidence of the limitations and non-limitations of human designers.  the second shows evidence of the limitations and non-limitations of evolution.

Which is why most people find the ID argument pretty flawed.  The very things that DON'T look like the way humans design things are the very things that are TYPICAL of things that have been optimised by evolution.  Which is a pretty good system.
If you have the time to fuck around with what is essentially trial and error in a constantly changing environment. And if you don't really give a rat's ass whether any of it succeeds or fails. Because there's no goal, no intent, no objective. Life is just a side show.

On the other hand, human designers, while they can and occasionally do use trial and error*, usually doesn't have the time to fuck around. They usually do give a rat's ass whether any of it succeeds or fails. And they usually do have definitive goals, intents and objectives.

And it's those differences that make the ID argument fall apart. For ID or BluffyDesign to work, one needs to state the intent, the goals and objectives. That's generally taken by Bluffy and his ilk to be to be advantageous to humanity. If so, then being an unlimited intellect with unlimited powers to make things happen, a lot of what's out there in the real work either seems to be indifferent of humanity or is actually deleterious to it. Take stars that are billions of light years away. What we see is the past, it's gone, done. And it's so far away now, both in time and space, it literally has no effect upon us one way or the other. So, what's the point. Why go to all that effort (of course, for a omnipotent god, it's no effort at all) for no purpose. Which brings up the issue of why would a god even bother? Why the fuckups? Being omniscient, it already knows the outcome of everything it does so there's no reason for any fuckups but more so, really no point in doing it at all. Sort of the ultimate Bluffoonic thought experiment. Either that or humanity is simply fooling itself that it's the purpose of all this. Which is not a bad assessment of what are often militantly ignorant narcissistic DK posterboys, thinking they are the apples of their god's eye.

So, either way, either we are the purpose of all this or we're simply narcissistically fooling ourselves that we are, it falls apart. If we are the purpose, this god is a bumbler. If we're fooling ourselves, well, we're just fooling ourselves. Sort of like Bluffy thinking his little hobby farm and hobo heaven is the start of SAVING THE WORLD, while he militantly refuses to even consider the ramifications of his "Plan" when it's expanded beyond his little plot of land.

*Edison was a great practitioner of trial and error. He would set up a very reductionist experiment, such as for the filaments of light bulbs, and doggedly try every material he could think of.

**I strongly recommend the Connections series by Edmund Burke.
Are we there yet?

Re: Manmade Software is Clumsy Compared to Godmade Software
Reply #28
Yeah ... organisms don't operate very well ... if God would just update the software ...
No one said "organisms don't operate very well".
Or anything like that.

Your strawman campaign continues.
It is profoundly dishonest.
Quote

Lolololol
idiot
Ahem.

Yes they DID say that.

Here's the whole convo which you dishonestly omitted part of ...

Quote
Also, this
Quote
Quote
The genome itself, via natural genome editing[19], generates large amounts of coherent new sequences and inserts these into DNA genomes without damaging essential protein-coding regions. This is not possible for any human-made software.
is nonsense. Software used to work like that, it turned out be be a spectacularly bad idea. We stopped doing it that way.

Quote
Hahahahahaha

Yeah ... organisms don't operate very well ... if God would just update the software ...

Lolololol
More...Quick EditQuote

  • RAFH
  • Have a life, already.
Re: Manmade Software is Clumsy Compared to Godmade Software
Reply #29
Not that Dave will understand what pingu just said. :(
Or what anyone else have or will say.
Are we there yet?

  • RAFH
  • Have a life, already.
Re: Manmade Software is Clumsy Compared to Godmade Software
Reply #30
"There is a new class of software that is quite a bit more like biological systems."

Wait.

Why?

I thought biological software was "bad design".

Wow.

Take the time to understand what people are saying. You'll garner a modicum of respect even if you disagree. As it is, you might as well be farting into the wind for all the sense you're making.
I'd say more like farting in a small closed closet, because, well, Bluffy likes the smell of his own farts.

Hey, he shits in a bucket in his make do shower. Then piles it up just outside his tarped pile of straw.
Are we there yet?

  • VoxRat
  • wtactualf
Re: Manmade Software is Clumsy Compared to Godmade Software
Reply #31
Some of what you say here is true.  One thing you seem to miss is - as Ayala observed in that quote that I wheel out every so often - most of the variation we see in organisms already exists within the respective genomes.  What does NOT exist previously within genomes is random stuff - mistakes - which the cell is designed to rigorously try to prevent.  And it does a damn good job, but not perfect as we have often discussed.  So mistakes happen and so we do get new variants.  And there are almost zero examples out of trillions of any of these random variants that can be in any way spun as being "beneficial" to the organism or the population.  The number may actually be zero now as we have learned more (for example, antibiotic resistance in bacteria used to be the "textbook example" of random mutations being beneficial but that crashed and burned). 

The more we learn about genomes, the more we realize that this amazing adaptive system that your describe HAS ALWAYS BEEN THERE.  IOW, we don't have any evidence of it having NOT been there ... EVER.  Any speculation that it wasn't at some point in the past is just that ... speculation ... and pretty stupid speculation at that.  That idea flies in the face of all reason and logic and experience.
::)  Pure preaching.  And pretty stupid preaching, at that.
"I understand Donald Trump better than many people because I really am a lot like him." - Dave Hawkins

  • Sea Star
  • Not an octohatter
Re: Manmade Software is Clumsy Compared to Godmade Software
Reply #32
Dave, there are presently 6 members and 4 guests reading this thread.
How many of us do you think take you seriously?
Hint - No more than 4.
Quote from: Dave Hawkins on Today at 07:50:40 AM
Lol
Sea Star has been trolling me this whole time.

  • VoxRat
  • wtactualf
Re: Manmade Software is Clumsy Compared to Godmade Software
Reply #33
Yeah ... organisms don't operate very well ... if God would just update the software ...
No one said "organisms don't operate very well".
Or anything like that.

Your strawman campaign continues.
It is profoundly dishonest.
Quote

Lolololol
idiot
Ahem.

Yes they DID say that.

Here's the whole convo which you dishonestly omitted part of ...

Quote
Also, this
Quote
Quote
The genome itself, via natural genome editing[19], generates large amounts of coherent new sequences and inserts these into DNA genomes without damaging essential protein-coding regions. This is not possible for any human-made software.
is nonsense. Software used to work like that, it turned out be be a spectacularly bad idea. We stopped doing it that way.

Quote
Hahahahahaha

Yeah ... organisms don't operate very well ... if God would just update the software ...

Lolololol
More...Quick EditQuote

Thanks for proving my point.
Nothing in there is anything remotely like your profoundly dishonest (mis)characterization:
Quote
organisms don't operate very well.

"I understand Donald Trump better than many people because I really am a lot like him." - Dave Hawkins

  • fredbear
  • Militantly Confused
Re: Manmade Software is Clumsy Compared to Godmade Software
Reply #34
This is Nested Hierarchies all over again. Convinced That everyone else is wrong, in ways he can't quite explain, Dave, pigeon-like, is running around knocking over chess prices and squawking victory.

:sad:
"...without considering any evidence at all - that my views are more likely - on average - to be correct.  Because the mainstream is almost always wrong" - Dave Hawkins

  • Sea Star
  • Not an octohatter
Re: Manmade Software is Clumsy Compared to Godmade Software
Reply #35
Some of what you say here is true.  One thing you seem to miss is - as Ayala observed in that quote that I wheel out every so often - most of the variation we see in organisms already exists within the respective genomes.  What does NOT exist previously within genomes is random stuff - mistakes - which the cell is designed to rigorously try to prevent.  And it does a damn good job, but not perfect as we have often discussed.  So mistakes happen and so we do get new variants.  And there are almost zero examples out of trillions of any of these random variants that can be in any way spun as being "beneficial" to the organism or the population.  The number may actually be zero now as we have learned more (for example, antibiotic resistance in bacteria used to be the "textbook example" of random mutations being beneficial but that crashed and burned). 

The more we learn about genomes, the more we realize that this amazing adaptive system that your describe HAS ALWAYS BEEN THERE.  IOW, we don't have any evidence of it having NOT been there ... EVER.  Any speculation that it wasn't at some point in the past is just that ... speculation ... and pretty stupid speculation at that.  That idea flies in the face of all reason and logic and experience.
::)  Pure preaching.  And pretty stupid preaching, at that.
No matter that its stupid. His imaginary audience is in awe at Dave's mighty words. Dave does have the best adjectives.
If we weren't Darwin-debased octohatters(most of us, anyway) we would not question his wisdom.
Quote from: Dave Hawkins on Today at 07:50:40 AM
Lol
Sea Star has been trolling me this whole time.

  • nesb
Re: Manmade Software is Clumsy Compared to Godmade Software
Reply #36
How does someone unironically give a thread this title?

  • RAFH
  • Have a life, already.
Re: Manmade Software is Clumsy Compared to Godmade Software
Reply #37
Yeah ... organisms don't operate very well ... if God would just update the software ...
No one said "organisms don't operate very well".
Or anything like that.

Your strawman campaign continues.
It is profoundly dishonest.
Quote

Lolololol
idiot
Ahem.

Yes they DID say that.

Here's the whole convo which you dishonestly omitted part of ...

Quote
Also, this
Quote
Quote
The genome itself, via natural genome editing[19], generates large amounts of coherent new sequences and inserts these into DNA genomes without damaging essential protein-coding regions. This is not possible for any human-made software.
is nonsense. Software used to work like that, it turned out be be a spectacularly bad idea. We stopped doing it that way.

Quote
Hahahahahaha

Yeah ... organisms don't operate very well ... if God would just update the software ...

Lolololol
More...Quick EditQuote

Um, Bluffy, you failed to cite your sources for those quotes. A typical dishonest tactic of yours. When Vox said nobody said that, he was clearly referring to people here in this forum, which is what you were referring to in your post that he was responding from. And he was clearly stating that nobody said "organisms don't operate very well".

The first quote was clearly not from one of us, the obvious point being it's got a footnote in it. Nor sure where that came from.
The second quote, from Saunt Taunga, was noting the statement in the quote quoted, that it was not possible for any human-made software to self-edit thus generating large amounts of coherent new sequences and inserts those into the program without damaging the functionality of the program, was nonsense, that previous human efforts to develop software that mimic certain aspects of evolution did not work very well, which is why efforts in that direction stopped.

You really do have serious and significant problems with comprehension.

BTW, the quote: "The genome itself, via natural genome editing[19], generates large amounts of coherent new sequences and inserts these into DNA genomes without damaging essential protein-coding regions." completely blows your notion that evolution, via mutations and selection is not possible. The authors are clearly stating is not only is possible but is a primary characteristic of evolution.

BTW2, simplicity is always the best route for design. Why make things any more complex than necessary. That's the joke you don't get about Rube Goldberg. It may work, but there's so many much easier ways to go about it. Evolution is Rube Goldberg, just as Edison was more Rube Goldbergish than not. He simply tried everything he could think of until he succeeded. Fortunately for him and the rest of us, he had plenty of time and money and associates to use that process. Had he known and utilized something about chemistry and molecular bonds and thermodynamics, he could have significantly reduced the potential materials to try as filaments.
  • Last Edit: February 24, 2018, 07:57:13 AM by RAFH
Are we there yet?

  • RAFH
  • Have a life, already.
Re: Manmade Software is Clumsy Compared to Godmade Software
Reply #38
Some of what you say here is true.  One thing you seem to miss is - as Ayala observed in that quote that I wheel out every so often - most of the variation we see in organisms already exists within the respective genomes.  What does NOT exist previously within genomes is random stuff - mistakes - which the cell is designed to rigorously try to prevent.  And it does a damn good job, but not perfect as we have often discussed.  So mistakes happen and so we do get new variants.  And there are almost zero examples out of trillions of any of these random variants that can be in any way spun as being "beneficial" to the organism or the population.  The number may actually be zero now as we have learned more (for example, antibiotic resistance in bacteria used to be the "textbook example" of random mutations being beneficial but that crashed and burned). 

The more we learn about genomes, the more we realize that this amazing adaptive system that your describe HAS ALWAYS BEEN THERE.  IOW, we don't have any evidence of it having NOT been there ... EVER.  Any speculation that it wasn't at some point in the past is just that ... speculation ... and pretty stupid speculation at that.  That idea flies in the face of all reason and logic and experience.
::)  Pure preaching.  And pretty stupid preaching, at that.
Well, of course it's stupid. This is Bluffy we are talking about. The BRILLIANT Bluffy with the high speed mind that runs circles around everyone else.

BTW, Bluffy, we do have evidence it was not there at one time. We have evidence there was no life on this planet, probably for at least a couple hundred million years. And then it was very, very simple. And gradually, very gradually, got more and more complex. Until it reached a sort of equilibrium with the physical world we live on. That keeps changing, and so does life. Some lineages get more complex, some get less, some new lineages develop, some die out.
Are we there yet?

Re: Manmade Software is Clumsy Compared to Godmade Software
Reply #39
Lots of chaff and flares here ...

To clear things up ... let's state things simply ...

1) ST started this whole thing by saying that "biological software" looks like it was poorly designed ... as if by a trial and error process
2) I countered by asking "how can you be qualified to judge it's quality when we are only familiar with 1.5% of it - the coding regions?"

I still have not got an answer to this ...

Re: Manmade Software is Clumsy Compared to Godmade Software
Reply #40
Also ... Life is mind numbingly complex ... so ST thinks that's a sign of bad design ...

But many man made items are also quite complex ... does this mean THOSE are bad design too?

  • borealis
  • Administrator
Re: Manmade Software is Clumsy Compared to Godmade Software
Reply #41
How does someone unironically give a thread this title?

Be a Biblical inerrantist who thinks the planet is less than 10,000 years old, Noah's Flood was real, and evolution is a lie
Be an arrogant egocentric authoritarian with an inflated belief in the superiority of one's own intellect.
Be a person who rarely reads anything through but just skims for affirming cherry picked quotes.
Be a male supremacist in everything but admission.
Be Dave Hawkins.

That would be your 'how'.

  • JonF
Re: Manmade Software is Clumsy Compared to Godmade Software
Reply #42
One thing you seem to miss is - as Ayala observed in that quote that I wheel out every so often - most of the variation we see in organisms already exists within the respective genomes.  What does NOT exist previously within genomes is random stuff - mistakes - which the cell is designed to rigorously try to prevent.  And it does a damn good job, but not perfect as we have often discussed.  So mistakes happen and so we do get new variants.  And there are almost zero examples out of trillions of any of these random variants that can be in any way spun as being "beneficial" to the organism or the population.
Sort of.  But the number of beneficial mutations is not zero, as you just acknowledged.

Quote
The number may actually be zero now as we have learned more (for example, antibiotic resistance in bacteria used to be the "textbook example" of random mutations being beneficial but that crashed and burned).
We've been over this before.  Antibiotic resistance in bacteria is one of many examples of beneficial ransom mutations.
"I would never consider my evaluation of his work to be fair minded unless I had actually read his own words." - Dave Hawkins

  • JonF
Re: Manmade Software is Clumsy Compared to Godmade Software
Reply #43
Lots of chaff and flares here ...

To clear things up ... let's state things simply ...

1) ST started this whole thing by saying that "biological software" looks like it was poorly designed ... as if by a trial and error process
2) I countered by asking "how can you be qualified to judge it's quality when we are only familiar with 1.5% of it - the coding regions?"
How are you qualified to discuss the topic?
"I would never consider my evaluation of his work to be fair minded unless I had actually read his own words." - Dave Hawkins

  • VoxRat
  • wtactualf
Re: Manmade Software is Clumsy Compared to Godmade Software
Reply #44
2) I countered by asking "how can you be qualified to judge it's quality when we are only familiar with 1.5% of it - the coding regions?"
I still have not got an answer to this ...
Before anyone could even conceivably answer this "question" (such as it is) you would need to clarify. A lot.
For starters:
- Who's "we" ?
- What does it mean for "us" (whoever "we" are) to be "familiar" ? With either the 1.5% or the 98.5% ? Do you assume that no one knows anything about non-coding DNA?
"I understand Donald Trump better than many people because I really am a lot like him." - Dave Hawkins

  • RAFH
  • Have a life, already.
Re: Manmade Software is Clumsy Compared to Godmade Software
Reply #45
Lots of chaff and flares here ...

To clear things up ... let's state things simply ...

1) ST started this whole thing by saying that "biological software" looks like it was poorly designed ... as if by a trial and error process
2) I countered by asking "how can you be qualified to judge it's quality when we are only familiar with 1.5% of it - the coding regions?"

I still have not got an answer to this ...
It does look poorly designed. Using the common definiton of "designed" as in was made with intent and with goals and objectives. It does look like it's more a result of trial and error.

As to your 1.5%, that's a mischaracterization.
We know a lot more about genomics than you apparently are aware of. And, no, one doesn't have to know the exact workings of every bit of DNA in every genome that exists or has ever existed to see the broad patterns. One can look at samples and get a pretty good idea of what's going on. Indeed, a lot of the examples are not even at the level of DNA. Many of those have been posted in threads here in TR.

What a bluffoon.

What you don't get is you are trying to impress upon biology the characteristics of a human-developed technology. While there are some parallels, the analogy, as with most of your analogies, is bad and taken way to far. Plus you still don't get that analogies are not evidence of anything but simply tools to help explain. Just because a particular rock is hot to the touch does not mean all rocks that are hot to the touch are hot to the touch for the same reasons. Some are volcanic, some have been laying in the hot sun. Some are surrounding a fire pit. Some are hot because they are being compressed. All are hot though. So, in the Bluffoonic mind, they are all hot for the same reason. Have to be. They're all rocks and they're all hot.
Are we there yet?

  • VoxRat
  • wtactualf
Re: Manmade Software is Clumsy Compared to Godmade Software
Reply #46
Also ... Life is mind numbingly complex ... so ST thinks that's a sign of bad design ...

But many man made items are also quite complex ... does this mean THOSE are bad design too?
You miss the point.
(Probably intentionally. That's part of the militant ignorance, as opposed to plain old ignorance, thing.)

ST is talking about complex solutions in lieu of obviously simpler solutions.
He spelled out exactly what he's talking about:
I'm thinking of things like the laryngeal nerve in giraffes, whale pelvises, marsupial birth and development of kidneys in mammals. These things have familiar patterns commonly found in badly designed sofware.
You, of course, (militantly) ignored that.
"I understand Donald Trump better than many people because I really am a lot like him." - Dave Hawkins

Re: Manmade Software is Clumsy Compared to Godmade Software
Reply #47

Quote
World J Biol Chem. 2014 Aug 26; 5(3): 275-278.
Published online 2014 Aug 26. doi:  10.4331/wjbc.v5.i3.275
PMCID: PMC4160521
Life is more than a computer running DNA software
František Baluška and Guenther Witzany

Are cellular organisms only robot-like computing machines that function strictly according to their algorithm-based programming? Or, rather, are they coordinated complex entities that share bio-communication properties that may vary according to different context-specific needs? Is DNA the unequivocal syntax for sequences out of which one can construct living cells, viruses and phages for a household appliance? Or is the superficial molecular syntax of DNA solely the result of evolution's long inserts and deletions of an abundance of various genetic parasites that shape host genomes? The most crucial questions are: do DNA sequences contain a hidden deep grammar structure that varies according to the meaning and context of environmental insults; do DNA sequences match with high fidelity environmental circumstances that led to epigenetic markings and memory? If yes, this would then mean that the identical DNA sequence may have various-even contradictory-meanings. In fact, this scenario is emerging as true[4-8].

EPIGENETICS: HIDDEN DEEP GRAMMAR
Interestingly, in complex genomes like humans, the coding genes are about 1.5% of the total genome whereas the abundance of non-coding RNAs are about 98.5%. This means Craig Venter's household appliance box could focus only on the 1.5% coding sequences. The DNA sequences of genomes do not represent 1:1 depictions of unequivocal coding structures such as genes, but in light of the variety of epigenetic markings-with its executives RNA editing and alternative splicing-can store a multitude of further meanings[4-8].

This means epigenetic marking saves energy costs like in human language. A limited repertoire of signs, and a limited number of rules to combine these signs correctly, enables signs using agents to generate an unlimited number of sentences with a superficial grammar in the visible text and an abundance of connotations by marking through gestures and other conscious and unconscious bodily expressions such as the movements of three hundred different eye muscles[9].

...

Therefore, DNA organized in chromatin is far more complex than the human-made "software system", except that we are confusing the algorithm-based simulation of real-life storage with the real life, the computer machines with the living cells and organisms, and the self-reproducing automatons with the real-life organisms that can replicate since the origins of life[5,9,14].

...

The genome itself, via natural genome editing[19], generates large amounts of coherent new sequences and inserts these into DNA genomes without damaging essential protein-coding regions. This is not possible for any human-made software.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4160521/
The best designs are simple.
Complexity is a sign of bad design.
Simplicity is hard. Complexity is something that happens if you don't prevent it.

Also, this
Quote
The genome itself, via natural genome editing[19], generates large amounts of coherent new sequences and inserts these into DNA genomes without damaging essential protein-coding regions. This is not possible for any human-made software.
is nonsense. Software used to work like that, it turned out be be a spectacularly bad idea. We stopped doing it that way.
Hahahahahaha

Yeah ... organisms don't operate very well ... if God would just update the software ...

Lolololol
Sure, organisms operate well most of the time. Some badly designed sofware also works very well. I know for a fact that functional software can be made by people who don't understand what they are doing. Something working wel is not proof of good design. Just keeping on trying stuff till it mostly works can produce functional software.

  • VoxRat
  • wtactualf
Re: Manmade Software is Clumsy Compared to Godmade Software
Reply #48
I know for a fact that functional software can be made by people who don't understand what they are doing.
I am living proof of that!  :wave:
"I understand Donald Trump better than many people because I really am a lot like him." - Dave Hawkins

Re: Manmade Software is Clumsy Compared to Godmade Software
Reply #49
How does someone unironically give a thread this title?

Have you not yet realised?  Dave is doing 8-D irony. He is so incredibly ironic that no-one can see it.